data_4YK5 # _model_server_result.job_id 9_IQ_VzPJWVBkPYZ7iOY7g _model_server_result.datetime_utc '2024-11-21 23:54:41' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4yk5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":204}' # _entry.id 4YK5 # _exptl.entry_id 4YK5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 264.315 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'hexyl beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 4YK5 _cell.length_a 76.6 _cell.length_b 76.6 _cell.length_c 123.736 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YK5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C12 H24 O6' _chem_comp.formula_weight 264.315 _chem_comp.id JZR _chem_comp.mon_nstd_flag n _chem_comp.name 'hexyl beta-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'hexyl beta-D-glucoside;hexyl D-glucoside;hexyl glucoside' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 O1 JZR sing 331 n n C1 C2 JZR sing 332 n n C1 O5 JZR sing 333 n n O1 C1' JZR sing 334 n n C2 O2 JZR sing 335 n n C2 C3 JZR sing 336 n n C3 O3 JZR sing 337 n n C3 C4 JZR sing 338 n n C4 O4 JZR sing 339 n n C4 C5 JZR sing 340 n n C5 O5 JZR sing 341 n n C5 C6 JZR sing 342 n n C6 O6 JZR sing 343 n n C1' C2' JZR sing 344 n n C2' C3' JZR sing 345 n n C3' C4' JZR sing 346 n n C4' C5' JZR sing 347 n n C5' C6' JZR sing 348 n n C1 H1 JZR sing 349 n n C2 H2 JZR sing 350 n n O2 HO2 JZR sing 351 n n C3 H3 JZR sing 352 n n O3 HO3 JZR sing 353 n n C4 H4 JZR sing 354 n n O4 HO4 JZR sing 355 n n C5 H5 JZR sing 356 n n C6 H61 JZR sing 357 n n C6 H62 JZR sing 358 n n O6 HO6 JZR sing 359 n n C1' H1' JZR sing 360 n n C1' "H1'A" JZR sing 361 n n C2' H2' JZR sing 362 n n C2' "H2'A" JZR sing 363 n n C3' H3' JZR sing 364 n n C3' "H3'A" JZR sing 365 n n C4' H4' JZR sing 366 n n C4' "H4'A" JZR sing 367 n n C5' H5' JZR sing 368 n n C5' "H5'A" JZR sing 369 n n C6' H6' JZR sing 370 n n C6' "H6'A" JZR sing 371 n n C6' "H6'B" JZR sing 372 n n # _atom_sites.entry_id 4YK5 _atom_sites.fract_transf_matrix[1][1] 0.013055 _atom_sites.fract_transf_matrix[1][2] 0.007537 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015074 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008082 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 4DV A 1 201 1 4DV SX1 . C 3 PG0 A 1 202 1 PG0 PG4 . D 4 GSH A 1 203 2 GSH GTT . E 5 JZR A 1 204 3 JZR BOG . F 6 BOG A 1 205 4 BOG BOG . G 7 PG4 A 1 206 5 PG4 PG4 . H 8 HOH A 1 301 81 HOH HOH . H 8 HOH A 2 302 63 HOH HOH . H 8 HOH A 3 303 37 HOH HOH . H 8 HOH A 4 304 33 HOH HOH . H 8 HOH A 5 305 12 HOH HOH . H 8 HOH A 6 306 18 HOH HOH . H 8 HOH A 7 307 23 HOH HOH . H 8 HOH A 8 308 31 HOH HOH . H 8 HOH A 9 309 10 HOH HOH . H 8 HOH A 10 310 87 HOH HOH . H 8 HOH A 11 311 144 HOH HOH . H 8 HOH A 12 312 96 HOH HOH . H 8 HOH A 13 313 32 HOH HOH . H 8 HOH A 14 314 16 HOH HOH . H 8 HOH A 15 315 34 HOH HOH . H 8 HOH A 16 316 58 HOH HOH . H 8 HOH A 17 317 64 HOH HOH . H 8 HOH A 18 318 22 HOH HOH . H 8 HOH A 19 319 47 HOH HOH . H 8 HOH A 20 320 20 HOH HOH . H 8 HOH A 21 321 7 HOH HOH . H 8 HOH A 22 322 51 HOH HOH . H 8 HOH A 23 323 6 HOH HOH . H 8 HOH A 24 324 9 HOH HOH . H 8 HOH A 25 325 19 HOH HOH . H 8 HOH A 26 326 55 HOH HOH . H 8 HOH A 27 327 74 HOH HOH . H 8 HOH A 28 328 44 HOH HOH . H 8 HOH A 29 329 43 HOH HOH . H 8 HOH A 30 330 27 HOH HOH . H 8 HOH A 31 331 26 HOH HOH . H 8 HOH A 32 332 108 HOH HOH . H 8 HOH A 33 333 50 HOH HOH . H 8 HOH A 34 334 59 HOH HOH . H 8 HOH A 35 335 105 HOH HOH . H 8 HOH A 36 336 41 HOH HOH . H 8 HOH A 37 337 110 HOH HOH . H 8 HOH A 38 338 57 HOH HOH . H 8 HOH A 39 339 121 HOH HOH . H 8 HOH A 40 340 17 HOH HOH . H 8 HOH A 41 341 29 HOH HOH . H 8 HOH A 42 342 91 HOH HOH . H 8 HOH A 43 343 24 HOH HOH . H 8 HOH A 44 344 15 HOH HOH . H 8 HOH A 45 345 122 HOH HOH . H 8 HOH A 46 346 13 HOH HOH . H 8 HOH A 47 347 14 HOH HOH . H 8 HOH A 48 348 77 HOH HOH . H 8 HOH A 49 349 38 HOH HOH . H 8 HOH A 50 350 124 HOH HOH . H 8 HOH A 51 351 88 HOH HOH . H 8 HOH A 52 352 48 HOH HOH . H 8 HOH A 53 353 90 HOH HOH . H 8 HOH A 54 354 130 HOH HOH . H 8 HOH A 55 355 113 HOH HOH . H 8 HOH A 56 356 123 HOH HOH . H 8 HOH A 57 357 84 HOH HOH . H 8 HOH A 58 358 139 HOH HOH . H 8 HOH A 59 359 116 HOH HOH . H 8 HOH A 60 360 36 HOH HOH . H 8 HOH A 61 361 71 HOH HOH . H 8 HOH A 62 362 107 HOH HOH . H 8 HOH A 63 363 35 HOH HOH . H 8 HOH A 64 364 70 HOH HOH . H 8 HOH A 65 365 3 HOH HOH . H 8 HOH A 66 366 80 HOH HOH . H 8 HOH A 67 367 1 HOH HOH . H 8 HOH A 68 368 2 HOH HOH . H 8 HOH A 69 369 4 HOH HOH . H 8 HOH A 70 370 5 HOH HOH . H 8 HOH A 71 371 8 HOH HOH . H 8 HOH A 72 372 11 HOH HOH . H 8 HOH A 73 373 21 HOH HOH . H 8 HOH A 74 374 25 HOH HOH . H 8 HOH A 75 375 28 HOH HOH . H 8 HOH A 76 376 30 HOH HOH . H 8 HOH A 77 377 39 HOH HOH . H 8 HOH A 78 378 40 HOH HOH . H 8 HOH A 79 379 42 HOH HOH . H 8 HOH A 80 380 45 HOH HOH . H 8 HOH A 81 381 46 HOH HOH . H 8 HOH A 82 382 49 HOH HOH . H 8 HOH A 83 383 52 HOH HOH . H 8 HOH A 84 384 53 HOH HOH . H 8 HOH A 85 385 54 HOH HOH . H 8 HOH A 86 386 56 HOH HOH . H 8 HOH A 87 387 60 HOH HOH . H 8 HOH A 88 388 61 HOH HOH . H 8 HOH A 89 389 62 HOH HOH . H 8 HOH A 90 390 65 HOH HOH . H 8 HOH A 91 391 66 HOH HOH . H 8 HOH A 92 392 67 HOH HOH . H 8 HOH A 93 393 68 HOH HOH . H 8 HOH A 94 394 69 HOH HOH . H 8 HOH A 95 395 72 HOH HOH . H 8 HOH A 96 396 73 HOH HOH . H 8 HOH A 97 397 75 HOH HOH . H 8 HOH A 98 398 76 HOH HOH . H 8 HOH A 99 399 78 HOH HOH . H 8 HOH A 100 400 79 HOH HOH . H 8 HOH A 101 401 82 HOH HOH . H 8 HOH A 102 402 83 HOH HOH . H 8 HOH A 103 403 85 HOH HOH . H 8 HOH A 104 404 86 HOH HOH . H 8 HOH A 105 405 89 HOH HOH . H 8 HOH A 106 406 92 HOH HOH . H 8 HOH A 107 407 93 HOH HOH . H 8 HOH A 108 408 94 HOH HOH . H 8 HOH A 109 409 95 HOH HOH . H 8 HOH A 110 410 97 HOH HOH . H 8 HOH A 111 411 98 HOH HOH . H 8 HOH A 112 412 99 HOH HOH . H 8 HOH A 113 413 100 HOH HOH . H 8 HOH A 114 414 101 HOH HOH . H 8 HOH A 115 415 102 HOH HOH . H 8 HOH A 116 416 103 HOH HOH . H 8 HOH A 117 417 104 HOH HOH . H 8 HOH A 118 418 106 HOH HOH . H 8 HOH A 119 419 109 HOH HOH . H 8 HOH A 120 420 111 HOH HOH . H 8 HOH A 121 421 112 HOH HOH . H 8 HOH A 122 422 114 HOH HOH . H 8 HOH A 123 423 115 HOH HOH . H 8 HOH A 124 424 117 HOH HOH . H 8 HOH A 125 425 118 HOH HOH . H 8 HOH A 126 426 119 HOH HOH . H 8 HOH A 127 427 120 HOH HOH . H 8 HOH A 128 428 125 HOH HOH . H 8 HOH A 129 429 126 HOH HOH . H 8 HOH A 130 430 127 HOH HOH . H 8 HOH A 131 431 128 HOH HOH . H 8 HOH A 132 432 129 HOH HOH . H 8 HOH A 133 433 131 HOH HOH . H 8 HOH A 134 434 132 HOH HOH . H 8 HOH A 135 435 133 HOH HOH . H 8 HOH A 136 436 134 HOH HOH . H 8 HOH A 137 437 135 HOH HOH . H 8 HOH A 138 438 136 HOH HOH . H 8 HOH A 139 439 137 HOH HOH . H 8 HOH A 140 440 138 HOH HOH . H 8 HOH A 141 441 140 HOH HOH . H 8 HOH A 142 442 141 HOH HOH . H 8 HOH A 143 443 142 HOH HOH . H 8 HOH A 144 444 143 HOH HOH . H 8 HOH A 145 445 145 HOH HOH . H 8 HOH A 146 446 146 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 JZR . . . E 5 10.028 19.983 9.964 1 32.49 ? C1 JZR 204 A 1 HETATM 2 O O1 JZR . . . E 5 9.971 19.21 11.161 1 31.21 ? O1 JZR 204 A 1 HETATM 3 C C2 JZR . . . E 5 10.053 19.05 8.753 1 30.07 ? C2 JZR 204 A 1 HETATM 4 O O2 JZR . . . E 5 11.259 18.282 8.767 1 34.14 ? O2 JZR 204 A 1 HETATM 5 C C3 JZR . . . E 5 9.985 19.842 7.448 1 30.58 ? C3 JZR 204 A 1 HETATM 6 O O3 JZR . . . E 5 9.818 18.945 6.342 1 34.78 ? O3 JZR 204 A 1 HETATM 7 C C4 JZR . . . E 5 8.845 20.857 7.462 1 32.61 ? C4 JZR 204 A 1 HETATM 8 O O4 JZR . . . E 5 8.972 21.708 6.319 1 33.28 ? O4 JZR 204 A 1 HETATM 9 C C5 JZR . . . E 5 8.863 21.689 8.748 1 33 ? C5 JZR 204 A 1 HETATM 10 O O5 JZR . . . E 5 8.877 20.829 9.894 1 35.22 ? O5 JZR 204 A 1 HETATM 11 C C6 JZR . . . E 5 7.648 22.603 8.849 1 31.85 ? C6 JZR 204 A 1 HETATM 12 O O6 JZR . . . E 5 6.459 21.831 9.055 1 32.69 ? O6 JZR 204 A 1 HETATM 13 C C1' JZR . . . E 5 10.47 19.911 12.299 1 34.85 ? C1' JZR 204 A 1 HETATM 14 C C2' JZR . . . E 5 9.985 19.22 13.569 1 31.09 ? C2' JZR 204 A 1 HETATM 15 C C3' JZR . . . E 5 10.08 20.155 14.769 1 48.45 ? C3' JZR 204 A 1 HETATM 16 C C4' JZR . . . E 5 10.192 19.365 16.067 1 50.69 ? C4' JZR 204 A 1 HETATM 17 C C5' JZR . . . E 5 9.696 20.188 17.25 1 57.52 ? C5' JZR 204 A 1 HETATM 18 C C6' JZR . . . E 5 8.409 19.604 17.82 1 62.19 ? C6' JZR 204 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #